feat: enable metadata edit of published projects and samples

fixes:  #1173

app/Actions/Project/UpdateProject.php

@@ -25,6 +25,7 @@ public function update(Project $project, array $input)
         Validator::make($input, [
             'name' => ['required', 'string', 'max:255',  Rule::unique('projects')
                 ->where('owner_id', $project->owner_id)->ignore($project->id), ],
+            'description' => ['required_if:is_public,"true"', 'min:20'],
             'license' => ['required_if:is_public,"true"'],
         ], $errorMessages)->validate();
 
@@ -107,7 +108,7 @@ public function update(Project $project, array $input)
             $validation = $project->validation;
 
             if (! $validation) {
-                $validation = new Validation();
+                $validation = new Validation;
                 $validation->save();
                 $project->validation()->associate($validation);
                 $project->save();

app/Actions/Study/UpdateStudy.php

@@ -53,7 +53,7 @@ public function update(Study $study, array $input)
             $license_id = $licenseExists ? $input['license_id'] : $study->license_id;
 
             if ($is_public == true) {
-                $release_date = Carbon::now()->timestamp;
+                $release_date = $study->release_date;
 
                 $sample = $study->sample;
                 $sampleIdentifier = $sample->identifier ? $sample->identifier : null;

app/Http/Controllers/ProjectController.php

@@ -16,6 +16,7 @@
 use App\Models\Study;
 use App\Models\User;
 use App\Models\Validation;
+use App\Services\DOI\DOIService;
 use Auth;
 use Illuminate\Auth\Access\AuthorizationException;
 use Illuminate\Contracts\Auth\StatefulGuard;
@@ -31,6 +32,29 @@
 
 class ProjectController extends Controller
 {
+    /**
+     * The DOI service instance.
+     *
+     * @var \App\Services\DOI\DOIService
+     */
+    protected $doiService;
+
+    /**
+     * Create a new class instance.
+     *
+     * @return void
+     */
+    /**
+     * Create a new class instance.
+     *
+     * @return void
+     */
+    public function __construct(DOIService $doiService)
+    {
+        // Assign the DOI service instance
+        $this->doiService = $doiService;
+    }
+
     public function publicProjectView(Request $request, $owner, $slug)
     {
         $user = User::where('username', $owner)->firstOrFail();
@@ -274,7 +298,7 @@ public function validation(Request $request, Project $project)
         $validation = $project->validation;
 
         if (! $validation) {
-            $validation = new Validation();
+            $validation = new Validation;
             $validation->save();
             $project->validation()->associate($validation);
             $project->save();
@@ -302,7 +326,7 @@ public function validationReport(Request $request, Project $project)
         $validation = $project->validation;
 
         if (! $validation) {
-            $validation = new Validation();
+            $validation = new Validation;
             $validation->save();
             $project->validation()->associate($validation);
             $project->save();
@@ -414,6 +438,10 @@ public function update(Request $request, UpdateProject $updater, Project $projec
         }
 
         $updater->update($project, $request->all());
+        if ($project->is_public) {
+            $project->updateDOIMetadata($this->doiService);
+            $project->addRelatedIdentifiers($this->doiService);
+        }
 
         return $request->wantsJson() ? new JsonResponse('', 200) : back()->with('success', 'Project updated successfully');
     }

app/Http/Controllers/StudyController.php

@@ -12,6 +12,7 @@
 use App\Models\Project;
 use App\Models\Sample;
 use App\Models\Study;
+use App\Services\DOI\DOIService;
 use Auth;
 use Illuminate\Auth\Access\AuthorizationException;
 use Illuminate\Contracts\Auth\StatefulGuard;
@@ -28,6 +29,29 @@
 
 class StudyController extends Controller
 {
+    /**
+     * The DOI service instance.
+     *
+     * @var \App\Services\DOI\DOIService
+     */
+    protected $doiService;
+
+    /**
+     * Create a new class instance.
+     *
+     * @return void
+     */
+    /**
+     * Create a new class instance.
+     *
+     * @return void
+     */
+    public function __construct(DOIService $doiService)
+    {
+        // Assign the DOI service instance
+        $this->doiService = $doiService;
+    }
+
     public function publicStudiesView(Request $request)
     {
         $moleculeId = $request->get('compound');
@@ -68,6 +92,10 @@ public function update(Request $request, UpdateStudy $updater, Study $study)
         $study = $study->fresh();
 
         $study->load(['datasets', 'sample.molecules', 'tags']);
+        if ($study->is_public) {
+            $study->updateDOIMetadata($this->doiService);
+            $study->addRelatedIdentifiers($this->doiService);
+        }
 
         return $request->wantsJson()
             ? new JsonResponse($study, 200)

app/Models/HasDOI.php

@@ -134,6 +134,10 @@ public function getMetadata()
             if ($this->project) {
                 $authors = $this->project->authors ? $this->project->authors : [];
                 $citations = $this->project->citations ? $this->project->citations : [];
+                foreach ($this->tags as &$tag) {
+                    $keyword = $tag->name;
+                    array_push($keywords, $keyword);
+                }
             }
 
         } elseif ($this instanceof Dataset) {

app/Policies/ProjectPolicy.php

@@ -65,7 +65,7 @@ public function createProject(User $user)
      */
     public function updateProject(User $user, Project $project)
     {
-        if ($project->is_public || $project->is_archived || $project->is_deleted || $project->is_published) {
+        if ($project->is_archived || $project->is_deleted) {
             return false;
         }
 

app/Policies/StudyPolicy.php

@@ -61,7 +61,7 @@ public function createStudy(User $user)
      */
     public function updateStudy(User $user, Study $study)
     {
-        if ($study->is_public || $study->is_archived || $study->is_deleted || $study->is_published || (! $study->is_published && $study->doi)) {
+        if ($study->is_archived || $study->is_deleted) {
             return false;
         }
 

resources/js/Pages/Project/Partials/Details.vue

@@ -330,7 +330,7 @@
                                                         "
                                                     />
                                                 </div>
-                                                <fieldset>
+                                                <!-- <fieldset>
                                                     <legend
                                                         class="text-sm font-medium text-gray-900"
                                                     >
@@ -388,7 +388,7 @@
                                                             </div>
                                                         </div>
                                                     </div>
-                                                </fieldset>
+                                                </fieldset> -->
                                             </div>
                                             <div>
                                                 <div v-if="form.is_public">
@@ -698,7 +698,7 @@
                                                                     form.license
                                                                 "
                                                                 :disabled="
-                                                                    !canUpdateProject
+                                                                    project.is_public
                                                                 "
                                                                 label="License"
                                                                 :items="
@@ -713,8 +713,16 @@
                                                         "
                                                         class="mt-2"
                                                     />
+                                                    <div
+                                                        class="mt-2 flex text-xs"
+                                                    >
+                                                        You can't change the
+                                                        licence once the project
+                                                        is public
+                                                    </div>
                                                 </div>
-                                                <div class="mt-6 flex text-sm">
+
+                                                <!-- <div class="mt-6 flex text-sm">
                                                     <a
                                                         target="_blank"
                                                         href="https://docs.nmrxiv.org/submission-guides/sharing.html"
@@ -729,7 +737,7 @@
                                                             sharing
                                                         </span>
                                                     </a>
-                                                </div>
+                                                </div> -->
                                                 <div
                                                     class="mt-4 flex text-sm mb-6"
                                                 >
@@ -756,36 +764,8 @@
                                         </div>
                                     </div>
                                 </div>
-                                <!--Footer-->
-                                <div
-                                    v-if="!form.is_public"
-                                    class="flex-shrink-0 px-4 py-4 flex justify-end"
-                                >
-                                    <jet-action-message
-                                        :on="form.recentlySuccessful"
-                                        class="mr-3 py-2 text-green-200"
-                                    >
-                                        Saved.
-                                    </jet-action-message>
-                                    <jet-secondary-button
-                                        type="button"
-                                        class="bg-white py-2 px-4 border border-gray-300 rounded-md shadow-sm text-sm font-medium text-gray-700 hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-gray-500"
-                                        @click="open = false"
-                                    >
-                                        Cancel
-                                    </jet-secondary-button>
-                                    <jet-button
-                                        v-if="canUpdateProject"
-                                        type="submit"
-                                        class="ml-4 inline-flex justify-center py-2 px-4 border border-transparent shadow-sm text-sm font-medium rounded-md text-white bg-gray-600 hover:bg-gray-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-gray-500"
-                                        @click="updateProject"
-                                    >
-                                        Save
-                                    </jet-button>
-                                </div>
-                                <!--Footer with confirmation-->
+
                                 <div
-                                    v-if="form.is_public && canUpdateProject"
                                     class="flex-shrink-0 px-4 py-4 flex justify-end"
                                 >
                                     <div class="flex items-center h-5">
@@ -802,11 +782,11 @@
                                         <label
                                             for="confirm"
                                             class="font-small text-red-700"
-                                            >I understand, if the project is
-                                            made public then all the underlying
-                                            studies and dataset will also be
-                                            made public and this version is no
-                                            longer editable.
+                                            >I understand, if the project
+                                            metadata is updated, the project
+                                            will keep its same doi, but the doi
+                                            will have new metadata and
+                                            therefore, a new metadata version.
                                         </label>
                                     </div>
                                     <jet-secondary-button
@@ -1053,12 +1033,12 @@ export default defineComponent({
             if (this.form.license) {
                 this.form.license_id = this.form.license.id;
             }
-            if (this.linkAccess) {
-                this.form.access = "link";
-                this.form.access_type = this.selectedAccessType.value;
-            } else {
-                this.form.access = "restricted";
-            }
+            // if (this.linkAccess) {
+            //     this.form.access = "link";
+            //     this.form.access_type = this.selectedAccessType.value;
+            // } else {
+            //     this.form.access = "restricted";
+            // }
             this.form.tags_array = this.form.tags.map((t) => t.text);
             if (this.form.tag != "") {
                 let tags = this.form.tag.split(",");

resources/js/Pages/Project/Show.vue

@@ -77,7 +77,7 @@
                                 <button
                                     v-if="canUpdateProject"
                                     type="button"
-                                    class="inline-flex items-center shadow-sm px-4 py-1.5 text-sm leading-5 font-medium rounded-full text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-teal-500"
+                                    class="inline-flex items-center shadow-sm px-4 py-1.5 ml-2 text-sm leading-5 font-medium rounded-full text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-teal-500"
                                     @click="toggleDetails"
                                 >
                                     <svg
@@ -306,10 +306,7 @@
                                 </span>
                             </div>
                         </div>
-                        <div
-                            v-if="!canUpdateProject"
-                            class="flex-nowrap right ml-auto"
-                        >
+                        <div class="flex-nowrap right ml-auto">
                             <img
                                 v-if="project.project_photo_url"
                                 :src="project.project_photo_url"
@@ -921,7 +918,7 @@
                                 License
                             </span>
                             <button
-                                v-if="canUpdateProject"
+                                v-if="canUpdateProject && !project.is_public"
                                 type="button"
                                 class="inline-flex items-center shadow-sm px-4 py-1.5 border border-gray-300 text-sm leading-5 font-medium rounded-full text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-teal-500"
                                 @click="toggleDetails"

resources/js/Pages/Study/About.vue

@@ -98,7 +98,7 @@
                                             License
                                         </span>
                                         <button
-                                            v-if="canUpdateStudy"
+                                            v-if="canUpdateStudy && !study.is_public"
                                             type="button"
                                             class="inline-flex items-center shadow-sm px-4 py-1.5 border border-gray-300 text-sm leading-5 font-medium rounded-full text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-teal-500"
                                             @click="openStudyDetailsPane"

resources/js/Pages/Study/Layout.vue

@@ -97,7 +97,7 @@
                                     <button
                                         v-if="canUpdateStudy"
                                         type="button"
-                                        class="inline-flex items-center shadow-sm px-4 py-1.5 text-sm leading-5 font-medium rounded-full text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-teal-500"
+                                        class="inline-flex items-center shadow-sm px-4 py-1.5 ml-2 text-sm leading-5 font-medium rounded-full text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-teal-500"
                                         @click="toggleDetails"
                                     >
                                         <svg